Infrastructure Updates

The Intel Compiler is now fully supported on Linux and Windows, both 32bit and 64bit; it builds faster binaries and supports some functionality not available in MSVC.

On Windows there is now experimental support for Clang/C2, the Microsoft version of the clang compiler.

Please see the manual for more information on how to use these compilers.

support deb/rpm/exe/dmg packages and SSE4+POPCNT binaries

Platforms:

full FreeBSD support

Ship UCRT, OPENMP and Intel DLLs for apps on windows

more apps available on Windows and some packaging fixes

Documentation Updates

Api Docs:

Tree-View by Module

Release 2.1.1

Minor release including major improvements of the manual, several library bug-fixes and changes in the build system. All library modules are backward compatible
with 2.1.0. For a complete list of changes visit GitHub.

Selected Bug Fixes

Tests:

delete automatically created temp directories in unit and app tests

demo tests: std::cout was not considered in tests

App Updates

Yara:

fall back to single-end mapping when paired-end library length distribution is neither given nor estimable

Release 2.0.2

Minor release including several library bug-fixes as well as better documentation and infrastructure.
All library modules are backward compatible with 2.0.1.
For a complete list of changes visit GitHub.

Release 2.0.1

Minor release including several library bug-fixes as well as better documentation and infrastructure.
All library modules are backward compatible with 2.0.0.
For a complete list of changes visit GitHub.

Library Bug Fixes

Basic:

Added AminoAcid symbol "O"

Disabled global exception handler by default

Sequence:

Added missing overloads for const Strings

Fixed and tested StringSet

Reworked STL containers adaption

Fixed several bugs in ModifiedStrings and ModifiedIterators

Stream:

Worked around I/O with std::string

Supported multi-stream gzip files produced by Illumina Casava

Fixed BgzfStream tell()

SeqIO:

Changed Raw file extension from .txt to .raw

BAM I/O:

Fixed BIN computation

Fixed a bug in jumpToOrphans()

Fixed internal concurrency problems

Fixed readBamHeader() to clear the BamHeader

Added assertions to writeRecord()

Added BamIndex::save() to save .bai files

Gff I/O:

Fixed parsing of comment lines

FragmentStore:

Fixed loading Gtf/Gff3 files

Index:

Fixed open() and save() for WT FMIndex

Added open() and save() for OpenAddressing QGramIndex

Seeds:

Fixed a bug in sparse chaining

Fixed a bug in banded chain alignment

Documentation Updates

Manual:

Fixed and improved several Tutorials and HowTos

Added version-aware links to the dox

Dox:

Added @datarace entity

Fixed broken links in "See Also" section

Fixed a problem with close button in the side pane

Documented class VirtualStream

Demos:

Restructured demos directory

Fixed several broken demos

Infrastructure Updates

Platform Support:

Added support for GCC 4.9 and Clang 3.7

Preliminary support for Clang 3.8 with OpenMP

Preliminary support for Visual Studio 2015

Preliminary support for FreeBSD 10.2

Build System:

Tested all demos

Upgraged TravisCI builds to run on Docker

Fixed Java detection

Release 2.0.0

Major release with many new features and applications.
Note, the majority of the modules are backward compatible to the previous version.
Some modules, e.g. I/O-modules, have some adapted easier-to-use or unified interfaces.